Turn an existing conda environment into a Singularity container

A single-cell RNAseq pipeline for 10X genomics data

The set of NGS processing pipelines used at Babraham

Experimental features for Nextflow

A simple Snakemake profile for Slurm without --cluster-config

Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark or bwa-meth + MethylDackel

A tool to map bisulfite converted sequence reads and determine cytosine methylation states

A (mostly) universal methylation extractor for BS-seq experiments.

Bismark-MethylDackel DNA methylation quantification pipeline in snakemake.

Uses `snakemake` to run `bismark` in a reproducible pipeline. Can be run locally, or on a cluster running the SLURM scheduler.

🐍 The MetricQ Python interface

Linux OTF2 Sampling - A Lightweight Node-Level Performance Monitoring Tool

Bring your single-cell data to life

CellGen IT documentation

An interactive explorer for single-cell transcriptomics data

Convert between AnnData and SingleCellExperiment

Workflow for single-cell RNA-seq analysis using Seurat

A scanpy extension to analyse single-cell TCR and BCR data.

CellRank: dynamics from multi-view single-cell data

A Python implementation of the DESeq2 pipeline for bulk RNA-seq DEA.

This repository contains tiles and data for the map of github

Finding surprising needles (=features) in haystacks (=single cell/spatial genomics data).

Interactive image stack viewing in jupyter notebooks based on ipycanvas and ipywidgets

Single cell analysis in the browser

https://www.sc-best-practices.org

Porting DESeq2 into python via rpy2